def write_mode(self, n, kT=units.kB * 300, nimages=30):
"""Write mode to trajectory file."""
mode = self.get_mode(n) * sqrt(kT / abs(self.hnu[n]))
p = self.atoms.positions.copy()
n %= 3 * len(self.indices)
traj = PickleTrajectory('%s.%d.traj' % (self.name, n), 'w')
calc = self.atoms.get_calculator()
self.atoms.set_calculator()
for x in np.linspace(0, 2 * pi, nimages, endpoint=False):
self.atoms.set_positions(p + sin(x) * mode)
traj.write(self.atoms)
self.atoms.set_positions(p)
self.atoms.set_calculator(calc)
traj.close()
def write(self, filename):
from ase_ext.io.trajectory import PickleTrajectory
traj = PickleTrajectory(filename, 'w', self)
traj.write()
traj.close()